Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria

Article


Fruzangohar, Mario, Ebrahimie, Esmaeil, Ogunniyi, Abiodun D., Mahdi, Layla K., Paton, James C. and Adelson, David L.. 2013. "Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria." PLoS One. 8 (3), pp. e58759-e58767. https://doi.org/10.1371/journal.pone.0058759
Article Title

Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria

ERA Journal ID39745
Article CategoryArticle
AuthorsFruzangohar, Mario (Author), Ebrahimie, Esmaeil (Author), Ogunniyi, Abiodun D. (Author), Mahdi, Layla K. (Author), Paton, James C. (Author) and Adelson, David L. (Author)
Journal TitlePLoS One
Journal Citation8 (3), pp. e58759-e58767
Number of Pages9
Year2013
PublisherPublic Library of Science (PLoS)
Place of PublicationUnited States
ISSN1932-6203
Digital Object Identifier (DOI)https://doi.org/10.1371/journal.pone.0058759
Web Address (URL)http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3594149/pdf/pone.0058759.pdf
Abstract

The primary means of classifying new functions for genes and proteins relies on Gene Ontology (GO), which defines genes/proteins using a controlled vocabulary in terms of their Molecular Function, Biological Process and Cellular Component. The challenge is to present this information to researchers to compare and discover patterns in multiple datasets using visually comprehensible and user-friendly statistical reports. Importantly, while there are many GO resources available for eukaryotes, there are none suitable for simultaneous, graphical and statistical comparison between multiple datasets. In addition, none of them supports comprehensive resources for bacteria. By using Streptococcus pneumoniae as a model, we identified and collected GO resources including genes, proteins, taxonomy and GO relationships from NCBI, UniProt and GO organisations. Then, we designed database tables in PostgreSQL database server and developed a Java application to extract data from source files and loaded into database automatically. We developed a PHP web application based on Model-View-Control architecture, used a specific data structure as well as current and novel algorithms to estimate GO graphs parameters. We designed different navigation and visualization methods on the graphs and integrated these into graphical reports. This tool is particularly significant when comparing GO groups between multiple samples (including those of pathogenic bacteria) from different sources simultaneously. Comparing GO protein distribution among up- or downregulated genes from different samples can improve understanding of biological pathways, and mechanism(s) of infection. It can also aid in the discovery of genes associated with specific function(s) for investigation as a novel vaccine or therapeutic targets.

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Is original form ofCorrection: Comparative GO: A Web Application for Comparative Gene Ontology and Gene Ontology-Based Gene Selection in Bacteria
ANZSRC Field of Research 2020310704. Microbial genetics
460103. Applications in life sciences
Byline AffiliationsUniversity of Adelaide
Institution of OriginUniversity of Southern Queensland
Funding source
NHMRC
Grant ID
627142
Funding source
NHMRC
Grant ID
565526
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